Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations
Yao-ban Chan, Vincent Ranwez, Celine Scornavaccac
JOURNAL OF THEORETICAL BIOLOGY | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | Published : 2017
Gene trees and species trees can be discordant due to several processes. Standard models of reconciliations consider macro-evolutionary events at the gene level: duplications, losses and transfers of genes. However, another common source of gene tree-species tree discordance is incomplete lineage sorting (ILS), whereby gene divergences corresponding to speciations occur "out of order". However, ILS is seldom considered in reconciliation models. In this paper, we devise a unified formal IDTL reconciliation model which includes all the above mentioned processes. We show how to properly cost ILS under this model, and then give a fixed-parameter tractable (FPT) algorithm which calculates the mos..View full abstract
Awarded by French Agence Nationale de la Recherche Investissements d'Avenir/Bioinformatique
We would like to thank Nicolas Galtier and Edwin Jacox for fruitful discussions. This work was supported by the French Agence Nationale de la Recherche Investissements d'Avenir/Bioinformatique (ANR-10-BINF-01-01, ANR-10-BINF-01-02, Ancestrome).